Values#

class autode.values.Allocation(*args, **kwargs)#
__init__(x, units: Unit | str = Unit(mb))#

Allocation of memory or disk, must be non-negative

Parameters:

x (float)

Keyword Arguments:

units (autode.units.Unit | str | None)

implemented_units: Sequence[Unit] = [Unit(byte), Unit(mb), Unit(gb), Unit(tb)]#
class autode.values.Angle(*args, **kwargs)#

Angle in some units, defaults to radians

__init__(value, units=Unit(rad))#

Value constructor

Keyword Arguments:

units (autode.units.Unit | str | None)

implemented_units: Sequence[Unit] = [Unit(rad), Unit(°)]#
class autode.values.Coordinate(*args, units=Unit(Å))#
implemented_units: List[Unit] = [Unit(Å), Unit(bohr), Unit(nm), Unit(pm), Unit(m)]#
property x#

x component in Cartesian space

property y#

y component in Cartesian space

property z#

z component in Cartesian space

class autode.values.Coordinates(input_array, units=Unit(Å))#
implemented_units: List[Unit] = [Unit(Å), Unit(bohr), Unit(nm), Unit(pm), Unit(m)]#
class autode.values.Distance(*args, **kwargs)#

Distance in some units, defaults to Angstroms

__init__(value, units=Unit(Å))#

Value constructor

Keyword Arguments:

units (autode.units.Unit | str | None)

implemented_units: Sequence[Unit] = [Unit(Å), Unit(bohr), Unit(pm), Unit(nm), Unit(m)]#
class autode.values.Energies(*args: Energy)#

List of energies on an identical geometry/structure

__init__(*args: Energy)#
Parameters:

*args (autode.values.Energy)

append(other: Energy) None#

Add another energy to this list, if it does not already appear

copy()#

Return a shallow copy of the list.

first(energy_type: Type[Energy]) TypeEnergy | None#

Return the last instance of a particular energy type in these list of energies

Returns:

Energy

Return type:

(autode.values.Energy | None)

property first_potential: PotentialEnergy | None#

First potential energy in this list

last(energy_type: Type[Energy]) TypeEnergy | None#

Return the last instance of a particular energy type in these list of energies

Returns:

Energy

Return type:

(autode.values.Energy | None)

property last_potential: PotentialEnergy | None#

First potential energy in this list

class autode.values.Energy(*args, **kwargs)#

Type of energy in some units e.g. Potential, Free etc. defaults to Hartrees

__init__(value: Any, units: Unit | str = Unit(Ha), method: Method | None = None, keywords: Keywords | None = None, estimated: bool = False)#

Energy as a value. Has a method_str attribute which is set using a method used to calculate the energy along with any keywords e.g. PBE0/def2-SVP used to calculate it

Parameters:
  • method (autode.wrappers.methods.Method)

  • keywords (autode.wrappers.keywords.Keywords | None) – Set of keywords which this energy has been calculated at

  • estimated (bool) – Has this energy been estimated rather than calculated

implemented_units: Sequence[Unit] = [Unit(Ha), Unit(kcal mol-1), Unit(kJ mol-1), Unit(eV), Unit(J)]#
set_method_str(method: Method | None, keywords: Keywords | None) None#
class autode.values.EnergyArray(input_array: ndarray | Sequence, units: Unit | str | None = None)#
implemented_units: List[Unit] = [Unit(Ha), Unit(eV), Unit(kcal mol-1), Unit(kJ mol-1), Unit(J)]#
class autode.values.Enthalpy(H)#
class autode.values.EnthalpyCont(*args, **kwargs)#

Enthalpy contribution: H = E + H_cont

class autode.values.ForceConstant(*args, **kwargs)#
__init__(value, units=Unit(Ha Å^-2))#

Value constructor

Keyword Arguments:

units (autode.units.Unit | str | None)

implemented_units: Sequence[Unit] = [Unit(Ha Å^-2), Unit(Ha a0^-2), Unit(J m^-2), Unit(J ang^-2), Unit(J m^-2 kg^-1)]#
class autode.values.FreeEnergy(*args, **kwargs)#

(Gibbs) Free Energy (G)

class autode.values.FreeEnergyCont(*args, **kwargs)#

Free energy contribution: G = E + G_cont

class autode.values.Frequency(*args, **kwargs)#
__init__(value, units=Unit(cm ^ -1))#

Value constructor

Keyword Arguments:

units (autode.units.Unit | str | None)

implemented_units: Sequence[Unit] = [Unit(cm^-1), Unit(s^-1)]#
property is_imaginary: bool#

Imaginary frequencies are quoted as negative for simplicity

property real: Frequency#

A frequencies real (positive) value

class autode.values.Gradient(input_array, units=Unit(Ha(Å) ^ -1))#
implemented_units: List[Unit] = [Unit(Ha(Å)^-1), Unit(Ha(bohr)^-1), Unit(eV(Å)^-1), Unit(kcal mol-1(Å)^-1)]#
class autode.values.GradientRMS(*args, **kwargs)#
__init__(x, units: Unit | str = Unit(Ha(Å) ^ -1))#

Value constructor

Keyword Arguments:

units (autode.units.Unit | str | None)

implemented_units: Sequence[Unit] = [Unit(Ha(Å)^-1), Unit(Ha(bohr)^-1), Unit(eV(Å)^-1)]#
class autode.values.MWDistance(*args, **kwargs)#

Mass-weighted distance in some units, defaults to angstroms amu^(1/2)

__init__(value, units=Unit(Å amu^1/2))#

Value constructor

Keyword Arguments:

units (autode.units.Unit | str | None)

implemented_units: Sequence[Unit] = [Unit(Å amu^1/2)]#
class autode.values.Mass(*args, **kwargs)#
__init__(value, units=Unit(amu))#

Value constructor

Keyword Arguments:

units (autode.units.Unit | str | None)

implemented_units: Sequence[Unit] = [Unit(amu), Unit(kg), Unit(m_e)]#
class autode.values.MomentOfInertia(input_array, units=Unit(amu Å^2))#
implemented_units: List[Unit] = [Unit(amu Å^2), Unit(kg m^2)]#
class autode.values.PotentialEnergy(*args, **kwargs)#

Potential electronic energy (0 K, no zero-point energy)

class autode.values.Temperature(*args, **kwargs)#

Temperature in some units, defaults to Kelvin

__init__(value, units=Unit(kelvin))#

Value constructor

Keyword Arguments:

units (autode.units.Unit | str | None)

implemented_units: Sequence[Unit] = [Unit(kelvin), Unit(celsius)]#
class autode.values.Value(*args, **kwargs)#

Abstract base class for a value with a defined set of units, along with perhaps other attributes and methods

x = Value(0.0)

__init__(x: Any, units: Unit | str | None = None)#

Value constructor

Keyword Arguments:

units (autode.units.Unit | str | None)

copy()#

Copy this value, with its units

implemented_units: Sequence[Unit] = []#
to(units)#

Convert this value to a new unit, returning a copy

Return type:

(autode.values.Value)

Raises:

(TypeError)

class autode.values.ValueArray(input_array: ndarray | Sequence, units: Unit | str | None = None)#

Abstract base class for an array of values, e.g. gradients or a Hessian

implemented_units: List[Unit] = []#
to(units) Any#

Convert this array to a new unit, returning a copy

Return type:

(autode.values.ValueArray)

Raises:

(TypeError)

to_(units) None#

Convert this array into a set of new units, inplace. This will not copy the array

Raises:

(TypeError)

autode.values.method_string(method: Method | None, keywords: Keywords | None) str#

Create a method string for a method and the keywords